Cell based high throughput drug screening is a common starting point for the drug discovery and development process. Currently there is a push to combine complex cell culture systems with high throughput screening to provide more clinically applicable results, but there are mechanistic requirements inherent to HTS as well as material limitations that make this integration challenging. In this study we used a peptide based shear thinning hydrogel to create a synthetic extracellular scaffold to culture cells in 3D, study how the effectiveness of drugs can change based on the cells microenvironment, and show a preliminary implementation of the scaffold in a pilot drug screen targeting medulloblastoma. MAX8 is an amphiphilic beta-hairpin peptide that forms a hydrogel at physiological conditions. It was used as the synthetic cell scaffold. It was also modified to include various cell binding ligands to mimic proteins typically found in the cerebellum [RGDS (fibronectin), YIGSR (laminin), IKVAV (laminin)]. The shear thinning nature of the hydrogel allowed it to be used with unmodified HTS instrumentation. The RGDS tagged peptide was chosen as the primary cell scaffold due to its positive effects on cell proliferation and phenotype. 2,200 compounds were screened in the 384 well format against cells encapsulated in the hydrogel as well as cells growing on traditional 2D plastic. 80 compounds passed the first round of screening at a single point of concentration. 16-point dose response was done on those 80 compounds, of which 17 compounds validated. Three-dimensional cell based high throughput drug screening could be a powerful screening tool that allows researchers the ability to finely tune the cell microenvironment getting more clinically applicable data as a result. But there are challenges inherent to its full scale implementation and it is unlikely that there is a one size fits all solution for the large variety of existing diseases. We have shown the successful integration of a peptide based hydrogel into the high throughput format. We then used the cell model in a pilot screen which showed promising differences between traditional cell culture and the 3D encapsulated cell model.